pepcoil calculates the probability of a coiled-coil structure for windows of 28 residues through a protein sequence using the method of Lupas A, et al. (1991).

Here is a sample session with pepcoil:

% pepcoil
Input sequence: sw:gcn4_yeast
Window size [28]:
Output file [gcn4_yeast.pepcoil]:

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

-window (integer)

Window size.

[-outfile] (outfile)

Output filename.

Advanced qualifiers:

-[no]coil (boolean)

Report coiled coil regions.

-frame (boolean)

Show coil frameshifts.

-[no]other (boolean)

Report non coiled coil regions.